SNAP output for PDB entry 9f6k [SNAP web server]

PDB-id

9f6k; SNAP-derived features in text and JSON formats; DNAproDB

Class

replication

Method

cryo-EM (4.2 Å)

Summary

Human DNA polymerase epsilon bound to t-c mismatched DNA (frayed substrate state)

Reference

Roske JJ, Yeeles JTP (2024): "Structural basis for processive daughter-strand synthesis and proofreading by the human leading-strand DNA polymerase Pol epsilon." Nat.Struct.Mol.Biol. doi: 10.1038/s41594-024-01370-y.

Abstract

During chromosome replication, the nascent leading strand is synthesized by DNA polymerase epsilon (Pol ε), which associates with the sliding clamp processivity factor proliferating cell nuclear antigen (PCNA) to form a processive holoenzyme. For high-fidelity DNA synthesis, Pol ε relies on nucleotide selectivity and its proofreading ability to detect and excise a misincorporated nucleotide. Here, we present cryo-electron microscopy (cryo-EM) structures of human Pol ε in complex with PCNA, DNA and an incoming nucleotide, revealing how Pol ε associates with PCNA through its PCNA-interacting peptide box and additional unique features of its catalytic domain. Furthermore, by solving a series of cryo-EM structures of Pol ε at a mismatch-containing DNA, we elucidate how Pol ε senses and edits a misincorporated nucleotide. Our structures delineate steps along an intramolecular switching mechanism between polymerase and exonuclease activities, providing the basis for a proofreading mechanism in B-family replicative polymerases.